Hi noman87--
Tim is right that the closest you can fly to Chanute, Kansas is Joplin, Missouri. And Joplin only has flights from Dallas -- a couple per day. Joplin is about 140 kilometers from Chanute, though, and there isn't any public transportation from Joplin to Chanute. So you'd need to rent a car or have someone pick you up. Given your question about a train to Chanute, I'm wondering if perhaps car rental is not a good option for you.
The closest the train comes to Chanute is about 160 kilometers away in Lawrence, Kansas. Not sure if you're familiar with Chanute and that part of the country, but Chanute is a relatively small town (10,000 people) in a rather rural part of the country where public transportation is very limited.
Chanute does have scheduled bus service twice per day -- one bus coming southbound from Minneapolis, Des Moines and Kansas City, and the other bus coming northbound from Oklahoma City and Tulsa. From Karachi you can fly to any of those cities (with two connections) and catch the bus to Chanute there. However because the bus only goes once per day each direction, the flight times in from Karachi don't always align well with the time the bus departs for Chanute.
The bus coming from the north goes through Kansas City in the middle of the night, arriving at 2:30am and leaving at 4:00am. I've heard bad things about the Kansas City bus terminal and would not personally want to have to spend a lot of time there in the middle of the night -- likely there may be homeless people around, few if any places open to buy food, very few employees or security, etc. It's definitely a matter of perception, of course -- I'm sure the odds of actually being a victim of crime there are rather low. I'd be less concerned if your time there was during the day, especially being someone in a strange country. If this doesn't sound too concerning, though, you could fly into Des Moines or Kanas City:
--If you fly into Des Moines you'd arrive at 6:50pm and would need to take a taxi to the Des Moines bus station. The bus leaves at 11:15pm and gets to Chanute at 6:15am. But it stops in Kansas City from 2:30am to 4:00am and I'm not sure if you may stay on the bus or if you must sit in the terminal. My suggestion would be to stay on the bus if you are allowed to. The air fare from Karachi to Des Moines is about $1500.
--If you fly into Kansas City the cheapest flight arrives around 10:50pm and you would need to take a taxi to the Kansas City bus station. You'd probably get there around midnight and have 4 hours to wait until the bus left at 4:00am. The lowest fare I saw from Karachi to Kansas City was close to $1250 on that day but if that fare isn't available when you book most other options are in the $1600-$2200 range. This could be the cheapest, and the bus ride from Kansas City to Chanute is only a little over 2 hours. But I am not keen about suggesting someone spend 4 hours in the Kansas City bus station.
The other option is to come into Chanute from the south, meaning flying into Oklahoma City or Tulsa. I'd suggest flying into Tulsa as it is only about 2.5 hour bus ride from Tulsa to Chanute. The flight gets into Tulsa at 7:40pm and the bus does not leave until 2:00pm the next afternoon. You'd need to take a taxi from the hotel to the bus station. Fare into Tulsa and Oklahoma City are more like $2100-$2500.
The bus company which serves Chanute is Jefferson Lines. The bus ticket to Chanute is in the $35-$75 dollar range depending on what city out fly into.
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Okay, now that I've typed all this, I think I have found a better option for you than taking the bus. You can get a car service or a dedicated van which will take you from the Kansas City Airport to Chanute. Kansas City. Here are some examples:
5 Guys Transportation offers a dedicated van service. They quote a fare of $260 for the van from Kansas City Airport to Chanute -- the van holds up to 6 people and the cost is the same no matter if you're alone or if you have other people with you.
http://www.flykci.com/Link.asp?IdS=0...ortation%2Ecom
Aero Shuttle Express quotes $220 to Chanute, again in a van or car which is just for your an your party (if you're not traveling alone.)
http://www.flykci.com/Link.asp?IdS=0...huttlekc%2Ecom
Elite Shuttle is another similar option, though you must e-mail them for a quote to know their fare to Chanute.
http://www.flykci.com/Link.asp?IdS=0...tlekc%2Ecom%2F
The nice thing about all of these sorts of services is that you're hiring them to transport you specifically. If you're late, they wait for you. You don't have to share it with anyone or make extra stops. And they will take you exactly where you need to go in Chanute.
The air fare to Kansas City is cheaper than some of the other options, with some fares as cheap as about $1250. Adding on the cost of the shuttle from the Kansas City Airport to Chanute is around $1500, and that's still similar or less expensive than air fare along to some of the other options like Tulsa or Oklahoma City. And you don't need to get a hotel room, get a taxi, and/or worry about a scary bus terminal or how late the bus is running.
Note that Kansas City Airport is nothing to be concerned about. It's the bus station that I'd avoid in the middle of the night.
I think your best bet is flying into Kansas City and getting a shuttle service to take you to Chanute. After 22-25 hours flying from Karachi to the US it will probably be nice to have someone waiting for you with a car for those last two hours to Chanute, not hours of waiting for a bus (which may not be on time) in a rough bus terminal.
You definitely must reserve these services ahead of time. Given the length and complexity of your journey, I'd suggest making sure they know your flight information, that you have a way to contact them, etc. I'd hate to have your flight run late and then you don't have a cell phone which works in the US, or don't have a phone number to call them, etc. Dedicated shuttle services like this are usually very good and accommodating.
Good luck!